Anopheles gambiae s.s. is subject to an ongoing speciation process which has resulted in increased malaria transmission spatially and temporally. Ecological adaptation associated with the speciation process has allowed exploitation of environments that formerly excluded A. gambiae: arid seasons and zones subject to irrigation for agriculture. It has been assumed that the arid-adapted incipient species (A. gambiae form M) shifted larval habitats from rain-dependent pools and puddles characteristic of A. gambiae form S to anthropogenic breeding sites associated with irrigation. However, the relevant ecological features used by the M and S forms to partition their environment at different spatial scales and developmental stages have not been established. We aim to study ecological adaptation at phenotypic and genotypic levels because we believe that this phenomenon is central to what makes A. gambiae the most efficient vector of malaria, and that an understanding of how it works will expose novel targets for control. We will complement ecological field studies of A. gambiae M and S at different spatial scales with a population genomic examination of adaptation based on the completed A. gambiae genome sequence and high throughput screening techniques. Toward the ultimate goal of identifying genes underlying complex ecophenotypes, we will apply a "topdown" approach in which key ecological differences between M and S will be carefully defined, and a "bottom-up" approach involving multilocus genome scans for candidate regions likely to be associated with ecological divergence of M and S. Within this framework, we propose the following specific aims: (1) Validate the hypothesis that M and S partition their habitat, and characterize the realized niche of each form at different spatial scales; (2) Define the spatial and temporal patterns of chromosomal polymorphism within M and S in relation to environmental heterogeneities; and (3) Identify genomic regions potentially associated with differential adaptations of M and S.